CHANGELOG.rst 36.2 KB
Newer Older
Paul McCarthy's avatar
Paul McCarthy committed
1
2
This document contains the ``fslpy`` release history in reverse chronological
order.
Paul McCarthy's avatar
Paul McCarthy committed
3
4


Paul McCarthy's avatar
Paul McCarthy committed
5
6
3.3.0 (Tuesday 22nd September 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
7
8
9
10
11
12
13
14


Added
^^^^^

* New ported versions of various core FSL tools, including ``imrm``, ``imln``,
  ``imtest``, ``fsl_abspath``, ``remove_ext``, ``Text2Vest``, and
  ``Vest2Text``.
Paul McCarthy's avatar
Paul McCarthy committed
15
* New :func:`.gps` function, wrapping the FSL ``gps`` command.
Paul McCarthy's avatar
Paul McCarthy committed
16
* New :func:`.vest.loadVestFile` and :func:`.vest.generateVest` functions.
Paul McCarthy's avatar
Paul McCarthy committed
17
18
19
20
21
22
23


Changed
^^^^^^^


* Updates to the BIDS filetree specification.
Paul McCarthy's avatar
Paul McCarthy committed
24
25


Paul McCarthy's avatar
Paul McCarthy committed
26
27
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
28
29


Paul McCarthy's avatar
Paul McCarthy committed
30
31
32
* The :class:`.CoefficientField` class now works with alternate reference
  images (i.e. a reference image with different dimensions to that which
  was originally used when the non-linear transformation was calculated).
Paul McCarthy's avatar
Paul McCarthy committed
33
34


Paul McCarthy's avatar
Paul McCarthy committed
35
36
37
38
39
40
41
42
43
44
45
3.2.2 (Thursday 9th July 2020)
------------------------------


Changed
^^^^^^^


* The :func:`.fslsub.func_to_cmd` function allows more fine-grained control
  over whether the script file is removed after the job has finished running.

Paul McCarthy's avatar
Paul McCarthy committed
46
47
48
49
50
51
52
53
54
55
56
57

3.2.1 (Tuesday 23rd June 2020)
------------------------------


Changed
^^^^^^^


* Minor updates to documentation.


Paul McCarthy's avatar
Paul McCarthy committed
58
59
60
61
62
63
64
65
66
67
3.2.0 (Thursday 11th June 2020)
-------------------------------


Added
^^^^^


* A new :func:`.fslsub.hold` function to wait on previously submitted jobs, to
  be used in place of the ``wait`` function.
Paul McCarthy's avatar
Paul McCarthy committed
68
69
70
71
72
73
74
75
76
77
78


Removed
^^^^^^^


* The :func:`.fslsub.wait` (and :func:`.run.wait`) function has been removed, as
  repeated calls to ``qstat`` can adversely affect the cluster job submission
  system.


Paul McCarthy's avatar
Paul McCarthy committed
79
80
3.1.0 (Thursday 21st May 2020)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
81
82


Paul McCarthy's avatar
Paul McCarthy committed
83
84
85
86
Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
87
* New :mod:`.cifti` module, providing classes and functions for working with
Paul McCarthy's avatar
Paul McCarthy committed
88
  `CIFTI <https://www.nitrc.org/projects/cifti/>`_ data.
Paul McCarthy's avatar
Paul McCarthy committed
89
90
91
92
93
94
* New :func:`.winpath` and :func:`wslpath` functions for working with paths
  when using FSL in a Windows Subsystem for Linux (WSL) environment.
* New :func:`.wslcmd` function for generating a path to a FSL command installed
  in a WSL environment.
* New :meth:`.Platform.fslwsl` attribute for detecting whether FSL is installed
  in a WSL environment.
Paul McCarthy's avatar
Paul McCarthy committed
95
96
97
98
99
100
101
102
103
104
105
106
* New :meth:`.Image.niftiDataType` property.
* The :class:`.FileTree` class has been updated to allow creation of
  deep copies via the new :meth:`.FileTree.copy` method.


Changed
^^^^^^^


* :func:`.Image` objects created from ``numpy`` arrays will be NIFTI1 or
  NIFTI2, depending on the value of the ``$FSLOUTPUTTYPE`` environment
  variable.
Paul McCarthy's avatar
Paul McCarthy committed
107
108


Paul McCarthy's avatar
Paul McCarthy committed
109
110
111
112
113
114
115
116
Fixed
^^^^^


* Updated the :func:`.fast` wrapper to support some single-character
  command-line flags.


Paul McCarthy's avatar
Paul McCarthy committed
117
118
119
120
121
122
123
124
125
126
3.0.1 (Wednesday 15th April 2020)
---------------------------------


Changed
^^^^^^^


* The :func:`.isMelodicDir` function now accepts directories that do not end
  with ``.ica``, as long as all required files are present.
Paul McCarthy's avatar
Paul McCarthy committed
127
128
* Added the ``dataclasses`` backport, so ``fslpy`` is now compatible with
  Python 3.6 again.
Paul McCarthy's avatar
Paul McCarthy committed
129
130


Paul McCarthy's avatar
Paul McCarthy committed
131
132
3.0.0 (Sunday 29th March 2020)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
133
134
135
136
137
138


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
139
140
* New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and
  :func:`applyxfm4D` commands.
Paul McCarthy's avatar
Paul McCarthy committed
141
142
143
* New ``firstDot`` option to the :func:`.path.getExt`,
  :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
  rudimentary support for double-barrelled filenames.
Paul McCarthy's avatar
Paul McCarthy committed
144
145
* The :func:`.nonlinear.applyDeformation` function now accepts a ``premat``
  affine, which is applied to the input image before the deformation field.
Paul McCarthy's avatar
Paul McCarthy committed
146
147
* New :class:`.SubmitParams` class, providing a higer level interface for
  cluster submission.
Paul McCarthy's avatar
Paul McCarthy committed
148
* New :meth:`.FileTree.load_json` and  :meth:`.FileTree.save_json` methods.
Paul McCarthy's avatar
Paul McCarthy committed
149

Paul McCarthy's avatar
Paul McCarthy committed
150

Paul McCarthy's avatar
Paul McCarthy committed
151
152
153
154
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
155
* ``fslpy`` now requires a minimum Python version of 3.7.
Paul McCarthy's avatar
Paul McCarthy committed
156
* The default value for the ``partial_fill`` option to :meth:`.FileTree.read`
Paul McCarthy's avatar
Paul McCarthy committed
157
158
159
  has been changed to ``False``. Accordingly, the :class:`.FileTreeQuery`
  calls the :meth:`.FileTree.partial_fill` method on the ``FileTree`` it is
  given.
Paul McCarthy's avatar
Paul McCarthy committed
160
161
* The :func:`.gifti.relatedFiles` function now supports files with
  BIDS-style naming conventions.
Paul McCarthy's avatar
Paul McCarthy committed
162
163
164
165
166
* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any
  additional keyword arguments to ``subprocess.Popen`` or, if ``submit=True``,
  to :func:`fslsub.submit`.
* The :func:`.fslsub.submit` function now accepts an ``env`` option, allowing
  environment variables to be specified.
Paul McCarthy's avatar
Paul McCarthy committed
167
168
* The :func:`.run.runfsl` function now raises an error on attempts to
  run a command which is not present in ``$FSLDIR/bin/`` (e.g. ``ls``).
Paul McCarthy's avatar
Paul McCarthy committed
169
170
171
* The :mod:`.bids` module has been updated to support files with any
  extension, not just those in the core BIDS specification (``.nii``,
  ``.nii.gz``, ``.json``, ``.tsv``).
Paul McCarthy's avatar
Paul McCarthy committed
172
173
174
175
176
177
178
* The return value of a function decorated with :func:`.fileOrImage`,
  :func:`.fileOrArray`, or :func:`.fileOrText` is now accessed via an attribute
  called ``stdout``, instead of ``output``.
* Output files of functions decorated with :func:`.fileOrImage`,
  :func:`.fileOrArray`, or :func:`.fileOrText`, which have been loaded via the
  :attr:`.LOAD` symbol, can now be accessed as attributes of the returned
  results object, in addition to being accessed as dict items.
Paul McCarthy's avatar
Paul McCarthy committed
179
* Wrapper functions decorated with the :func:`.fileOrImage`,
Paul McCarthy's avatar
Paul McCarthy committed
180
  :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
Paul McCarthy's avatar
Paul McCarthy committed
181
182
183
184
  arguments and return values through unchanged if an argument called ``submit``
  is passed in, and is set to ``True`` (or any non-``False``
  value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if
  any in-memory objects or ``LOAD`` symbols are passed.
Paul McCarthy's avatar
Paul McCarthy committed
185
186
187
* The :func:`.fileOrText` decorator has been updated to work with input
  values - file paths must be passed in as ``pathlib.Path`` objects, so they
  can be differentiated from input values.
Paul McCarthy's avatar
Paul McCarthy committed
188
189
* Loaded :class:`.Image` objects returned by :mod:`fsl.wrappers` functions
  are now named according to the wrapper function argument name.
Paul McCarthy's avatar
Paul McCarthy committed
190
191


Paul McCarthy's avatar
Paul McCarthy committed
192
193
194
195
196
197
198
Fixed
^^^^^


* Updated the :func:`.prepareArgs` function to use ``shlex.split`` when
  preparing shell command arguments, instead of performing a naive whitespace
  split.
Paul McCarthy's avatar
Paul McCarthy committed
199
200
* Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
  functions.
Paul McCarthy's avatar
Paul McCarthy committed
201
202
* Fixed the :func:`.DeformationField.transform` method so it works with
  a single set of coordinates.
Paul McCarthy's avatar
Paul McCarthy committed
203
204
* :class:`.Image` creation does not fail if ``loadMeta`` is set, and a
  sidecar file containing invalid JSON is present.
Paul McCarthy's avatar
Paul McCarthy committed
205

Paul McCarthy's avatar
Paul McCarthy committed
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
Removed
^^^^^^^


* Removed the deprecated ``.StatisticAtlas.proportions``,
  ``.StatisticAtlas.coordProportions``, and
  ``.StatisticAtlas.maskProportions`` methods.
* Removed the deprecated ``indexed`` option to :meth:`.Image.__init__`.
* Removed the deprecated ``.Image.resample`` method.
* Removed the deprecated ``.image.loadIndexedImageFile`` function.
* Removed the deprecatd ``.FileTreeQuery.short_names`` and
  ``.Match.short_name`` properties.
* Removed the deprecated ``.idle.inIdle``, ``.idle.cancelIdle``,
  ``.idle.idleReset``, ``.idle.getIdleTimeout``, and
  ``.idle.setIdleTimeout`` functions.
* Removed the deprecated ``resample.calculateMatrix`` function.


Paul McCarthy's avatar
Paul McCarthy committed
224
225
226
227
228
229
230
231
232
233
234
235
236
237
2.8.4 (Monday 2nd March 2020)
-----------------------------


Added
^^^^^


* Added a new ``partial_fill`` option to :meth:`.FileTree.read`, which
  effectively eliminates any variables which only have one value. This was
  added to accommodate some behavioural changes that were introduced in 2.8.2.



Paul McCarthy's avatar
Paul McCarthy committed
238
239
240
241
242
243
244
245
246
247
2.8.3 (Friday 28th February 2020)
---------------------------------


Fixed
^^^^^


* Fixed a bug in the :meth:`.Image.save` method.

Paul McCarthy's avatar
Paul McCarthy committed
248
249
250
251
252
253
254
255
256
257
258
259

2.8.2 (Thursday 27th February 2020)
-----------------------------------


Fixed
^^^^^


* Fixed some subtle bugs in the :func:`.filetree.utils.get_all` function.


Paul McCarthy's avatar
Paul McCarthy committed
260
261
2.8.1 (Thursday 20th February 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
262
263
264
265
266
267
268
269
270


Fixed
^^^^^


* Fixed a bug where an error would be raised on attempts to load an image file
  without a BIDS-compatible name from a BIDS-like directory.

Paul McCarthy's avatar
Paul McCarthy committed
271

Paul McCarthy's avatar
Paul McCarthy committed
272
273
2.8.0 (Wednesday 29th January 2020)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
274
275


Paul McCarthy's avatar
Paul McCarthy committed
276
277
278
279
280
281
282
283
Added
^^^^^


* New :meth:`.Nifti.adjust` method, for creating a copy of a :class:`.Nifti`
  header with adjusted shape, pixdims, and affine. This can be useful for
  creating a resampling reference.
* New :func:`.affine.rescale` function, for adjusting a scaling matrix.
Paul McCarthy's avatar
Paul McCarthy committed
284
285
* New :func:`.mghimage.voxToSurfMat` function, for creating a
  voxel-to-freesurfer affine transform from any image.
Paul McCarthy's avatar
Paul McCarthy committed
286
287


Paul McCarthy's avatar
Paul McCarthy committed
288
289
290
291
292
293
294
295
296
297
Changed
^^^^^^^


* The :class:`.ImageWrapper` now maintains its own image data cache, rather
  than depending on ``nibabel``.
* Internal changes to avoid using the deprecated
  ``nibabel.dataobj_images.DataobjImage.get_data`` method.


Paul McCarthy's avatar
Paul McCarthy committed
298
299
300
301
302
Fixed
^^^^^


* Improved the algorithm used by the :func:`.mesh.needsFixing` function.
Paul McCarthy's avatar
Paul McCarthy committed
303
304
* The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
  output specification.
Paul McCarthy's avatar
Paul McCarthy committed
305
306
* Fixed a bug in the :class:`.Mesh` class to prevent indices from being loaded
  as floating point type.
Paul McCarthy's avatar
Paul McCarthy committed
307
* Fixed a bug in the :func:`.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
308
309
* Fixed a bug in the :class:`.MGHImage` class, which was causing pixdims to
  be overridden by scales derived from the affine.
Paul McCarthy's avatar
Paul McCarthy committed
310
311


Paul McCarthy's avatar
Paul McCarthy committed
312
313
314
315
316
317
318
319
Deprecated
^^^^^^^^^^


* :func:`.calculateMatrix` - its functionality has been moved to the
  :func:`.affine.rescale` function.


Paul McCarthy's avatar
Paul McCarthy committed
320
321
2.7.0 (Wednesday 6th November 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
322
323
324
325
326
327
328
329
330


Added
^^^^^


* New ``until`` option to the :func:`.idle.block` function.
* New :meth:`.Idle.neverQueue` setting, which can be used to force all
  tasks passed to :func:`.idle.idle` to be executed synchronously.
Paul McCarthy's avatar
Paul McCarthy committed
331
332
* New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the
  value of :meth:`.IdleLoop.neverQueue`.
Paul McCarthy's avatar
Paul McCarthy committed
333
334
* New :mod:`.bids` module, containing a few simple functions for working with
  `BIDS <https://bids.neuroimaging.io>`_ datasets.
Paul McCarthy's avatar
Paul McCarthy committed
335
336
337
* New :func:`.image.loadMetadata` function, and ``loadMeta`` option to the
  :class:`.Image` class, to automatically find and load any sidecar JSON files
  associated with an image file.
Paul McCarthy's avatar
Paul McCarthy committed
338
339
340
341
342
343


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
344
* Internal reorganisation in the :mod:`.idle` module.
Paul McCarthy's avatar
Paul McCarthy committed
345
346


Paul McCarthy's avatar
Paul McCarthy committed
347
348
349
350
351
352
353
354
Fixed
^^^^^


* Fixed incorrect usage of ``setuptools.find_packages``, which was causing
  unit tests to be installed.


Paul McCarthy's avatar
Paul McCarthy committed
355
356
357
358
359
360
361
362
363
364
365
Deprecated
^^^^^^^^^^


* :func:`.idle.inIdle` - replaced by :meth:`.IdleLoop.inIdle`.
* :func:`.idle.cancelIdle` - replaced by :meth:`.IdleLoop.cancelIdle`.
* :func:`.idle.idleReser` - replaced by :meth:`.IdleLoop.idleReset`.
* :func:`.idle.getIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.
* :func:`.idle.setIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.


Paul McCarthy's avatar
Paul McCarthy committed
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
2.6.2 (Monday 7th October 2019)
-------------------------------


Changed
^^^^^^^


* Added a debugging hook in the :mod:`.idle` module.
* The :func:`.fslsub.submit` function is now more flexible in the way it
  accepts the command and input arguments.
* The :func:`.run.prepareArgs` function has been renamed (from
  ``_prepareArgs``).


Paul McCarthy's avatar
Paul McCarthy committed
381
382
383
384
385
386
387
388
389
390
391
392
2.6.1 (Thursday 19th September 2019)
------------------------------------


Changed
^^^^^^^


* ``fslpy`` is no longer tested against Python 3.5, and is now tested against
  Python 3.6, 3.7, and 3.8.


Paul McCarthy's avatar
Paul McCarthy committed
393
394
2.6.0 (Tuesday 10th September 2019)
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
395
396


Paul McCarthy's avatar
Paul McCarthy committed
397
398
399
400
401
Added
^^^^^


* New :meth:`.Image.iscomplex` attribute.
Paul McCarthy's avatar
Paul McCarthy committed
402
* Support for a new ``Statistic`` atlas type.
Paul McCarthy's avatar
Paul McCarthy committed
403
404


Paul McCarthy's avatar
Paul McCarthy committed
405
406
407
408
409
410
Changed
^^^^^^^


* The :class:`.Cache` class has a new ``lru`` option, allowing it to be used
  as a least-recently-used cache.
Paul McCarthy's avatar
Paul McCarthy committed
411
412
* The :mod:`fsl.utils.filetree` module has been refactored to make it easier
  for the :mod:`.query` module to work with file tree hierarchies.
Paul McCarthy's avatar
Paul McCarthy committed
413
414
415
* The :meth:`.LabelAtlas.get` method has a new ``binary`` flag, allowing
  either a binary mask, or a mask with the original label value, to be
  returned.
Paul McCarthy's avatar
Paul McCarthy committed
416
417
* The :mod:`.dicom` module has been updated to work with the latest version of
  ``dcm2niix``.
Paul McCarthy's avatar
Paul McCarthy committed
418
419
420
421
422
423
424
425
426
427
428


Deprecated
^^^^^^^^^^


* :meth:`.ProbabilisticAtlas.proportions`,
  :meth:`.ProbabilisticAtlas.maskProportions`, and
  :meth:`.ProbabilisticAtlas.labelProportions` have been deprecated in favour
  of :meth:`.StatisticAtlas.values`, :meth:`.StatisticAtlas.maskValues`, and
  :meth:`.StatisticAtlas.labelValues`
Paul McCarthy's avatar
Paul McCarthy committed
429
430


Paul McCarthy's avatar
Paul McCarthy committed
431
432
2.5.0 (Tuesday 6th August 2019)
-------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
433
434


Paul McCarthy's avatar
Paul McCarthy committed
435
436
437
438
Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
439
440
441
442
443
444
445
446
447
448
449
450
* New :meth:`.Image.getAffine` method, for retrieving an affine between any of
  the voxel, FSL, or world coordinate systems.
* New :mod:`fsl.transforms` package, which contains classes and functions for
  working with linear and non-linear FLIRT and FNIRT transformations.
* New static methods :meth:`.Nifti.determineShape`,
  :meth:`.Nifti.determineAffine`, :meth:`.Nifti.generateAffines`, and
  :meth:`.Nifti.identifyAffine`.
* New prototype :mod:`fsl.transforms.x5`  module, for reading/writing linear
  and non-linear X5 files (*preliminary release, subject to change*).
* New prototype :mod:`.fsl_convert_x5` :mod:`.fsl_apply_x5` programs, for
  working with X5 transformations (*preliminary release, subject to change*).

Paul McCarthy's avatar
Paul McCarthy committed
451
452


Paul McCarthy's avatar
Paul McCarthy committed
453
454
455
456
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
457
458
* The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more
  lenient.
Paul McCarthy's avatar
Paul McCarthy committed
459
460
461
462
463
464
465
* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.


Deprecated
^^^^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
466
* The :mod:`fsl.utils.transform` module has been deprecated; its functions can
Paul McCarthy's avatar
Paul McCarthy committed
467
468
  now be found in the :mod:`fsl.transforms.affine` and
  :mod:`fsl.transform.flirt` modules.
Paul McCarthy's avatar
Paul McCarthy committed
469
470


Paul McCarthy's avatar
Paul McCarthy committed
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
2.4.0 (Wednesday July 24th 2019)
--------------------------------


Added
^^^^^


* New :mod:`.image.roi` module, for extracting an ROI of an image, or expanding
  its field-of-view.


Changed
^^^^^^^


* The :mod:`.resample_image` script has been updated to support resampling of
  images with more than 3 dimensions.


Paul McCarthy's avatar
Paul McCarthy committed
491
492
493
494
495
496
497
498
499
500
501
2.3.1 (Friday July 5th 2019)
----------------------------


Fixed
^^^^^


* The :class:`.Bitmap` class now supports greyscale images and palette images.


Paul McCarthy's avatar
Paul McCarthy committed
502
503
2.3.0 (Tuesday June 25th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
504
505
506
507
508
509


Added
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
510
511
512
513
514
* New :class:`.Bitmap` class, for loading bitmap images. The
  :meth:`.Bitmap.asImage` method can be used to convert a ``Bitmap`` into
  an :class:`.Image`.
* The :class:`.Image` class now has support for the ``RGB24`` and ``RGBA32``
  NIfTI data types.
Paul McCarthy's avatar
Paul McCarthy committed
515
516
* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
  images.
Paul McCarthy's avatar
Paul McCarthy committed
517
518
519
520
521
522
523
524
525
526
527
528
529
530
* New :meth:`.LabelAtlas.get` and :meth:`ProbabilisticAtlas.get` methods,
  which return an :class:`.Image` for a specific region.
* The :meth:`.AtlasDescription.find` method also now a ``name`` parameter,
  allowing labels to be looked up by name.
* New :meth:`.FileTree.defines` and :meth:`.FileTree.on_disk` methods, to
  replace the :func:`.FileTree.exists` method.


Fixed
^^^^^


* The :func:`.makeWriteable` function will always create a copy of an
  ``array`` if its base is a ``bytes`` object.
Paul McCarthy's avatar
Paul McCarthy committed
531
* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
Paul McCarthy's avatar
Paul McCarthy committed
532
533
* Fixed a bug in the :meth:`.Mesh.addVertices` method where the wrong face
  normals could be used for newly added vertex sets.
Paul McCarthy's avatar
Paul McCarthy committed
534
535


Paul McCarthy's avatar
Paul McCarthy committed
536
537
2.2.0 (Wednesday May 8th 2019)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
538
539


Paul McCarthy's avatar
Paul McCarthy committed
540
541
542
543
544
545
546
547
548
549
550
551
552
Added
^^^^^


* New :mod:`.resample_image` script.
* New :mod:`.resample` module (replacing the :func:`.Image.resample` method),
  containing functions to resample an :class:`.Image`.
* New :func:`.resample.resampleToPixdim` and
  :func:`.resample.resampleToReference` functions, convenience wrappers around
  :func:`.resample.resample`.
* New :func:`.idle.block` function.


Paul McCarthy's avatar
Paul McCarthy committed
553
554
555
556
Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
557
558
559
560
561
562
563
* The :func:`.resample` function (formerly :meth:`.Image.resample`) now
  accepts ``origin`` and ``matrix`` parameters, which can be used to adjust
  the alignment of the voxel grids of the input and output images.
* The :func:`.transform.decompose` function now accepts both ``(3, 3)``
  and ``(4, 4)`` matrices.


Paul McCarthy's avatar
Paul McCarthy committed
564
565
566
567
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
568
* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Paul McCarthy's avatar
Paul McCarthy committed
569
570


Paul McCarthy's avatar
Paul McCarthy committed
571
572
573
574
575
576
Deprecated
^^^^^^^^^^


* The :meth:`.Image.resample` method has been deprecated in favour of the
  :func:`.resample.resample` function.
Paul McCarthy's avatar
Paul McCarthy committed
577
578


Paul McCarthy's avatar
Paul McCarthy committed
579
580
2.1.0 (Saturday April 13th 2019)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
581
582
583
584
585
586
587
588


Added
^^^^^


* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
  Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
589
590
* New :func:`.makeWriteable` function which ensures that a ``numpy.array`` is
  writeable, and creates a copy if necessary
Paul McCarthy's avatar
Paul McCarthy committed
591
592


Paul McCarthy's avatar
Paul McCarthy committed
593
594
595
596
597
Changed
^^^^^^^


* The :class:`.GiftiMesh` class no longer creates copies of the mesh
Paul McCarthy's avatar
Paul McCarthy committed
598
599
  vertex/index arrays. This means that, these arrays will be flagged as
  read-only.
Paul McCarthy's avatar
Paul McCarthy committed
600
601
602
* The :class:`.Mesh` class handles vertex data sets requiring different
  triangle unwinding orders, at the cost of potentially having to store
  two copies of the mesh indices.
Paul McCarthy's avatar
Paul McCarthy committed
603
604


Paul McCarthy's avatar
Paul McCarthy committed
605
606
607
608
609
610
611
612
613
Fixed
^^^^^


* The :class:`.FeatDesign` class now handles "compressed" voxelwise EV files,
  such as those generated by `PNM
  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PNM>`_.


Paul McCarthy's avatar
Paul McCarthy committed
614
615
616
617
618
619
620
621
622
623
624
625
2.0.1 (Monday April 1st 2019)
-----------------------------


Fixed
^^^^^


* Fixed a bug with the :func:`.gifti.relatedFiles` function returning
  duplicate files.


Paul McCarthy's avatar
Paul McCarthy committed
626
627
2.0.0 (Friday March 20th 2019)
------------------------------
628
629


630
631
632
Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
633
* New :mod:`fsl.utils.filetree` package for defining and working with
Paul McCarthy's avatar
Paul McCarthy committed
634
  file/directory templates (Michiel Cottaar).
Paul McCarthy's avatar
Paul McCarthy committed
635
* Simple built-in :mod:`.deprecated` decorator.
Paul McCarthy's avatar
Paul McCarthy committed
636
* New :mod:`fsl.data.utils` module, which currently contains one function
637
  :func:`.guessType`, which guesses the data type of a file/directory path.
638
* New :func:`.commonBase` function for finding the common prefix of a set of
Paul McCarthy's avatar
Paul McCarthy committed
639
  file/directory paths.
640
641


642
643
644
Changed
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
645

646
* Removed support for Python 2.7 and 3.4.
647
648
649
* Minimum required version of ``nibabel`` is now 2.3.
* The :class:`.Image` class now fully delegates to ``nibabel`` for managing
  file handles.
Paul McCarthy's avatar
Paul McCarthy committed
650
* The :class:`.GiftiMesh` class can now load surface files which contain
Paul McCarthy's avatar
Paul McCarthy committed
651
652
653
  vertex data, and will accept surface files which end in ``.gii``, rather
  than requiring files which end in ``.surf.gii``.
* The ``name`` property of :class:`.Mesh` instances can now be updated.
Paul McCarthy's avatar
Paul McCarthy committed
654
655


Paul McCarthy's avatar
Paul McCarthy committed
656
657
658
659
660
661
Removed
^^^^^^^

* Many deprecated items removed.


Paul McCarthy's avatar
Paul McCarthy committed
662
663
664
665
666
667
668
669
Deprecated
^^^^^^^^^^


* Deprecated the :func:`.loadIndexedImageFile`  function, and the ``indexed``
  flag to the :class:`.Image` constructor.


Paul McCarthy's avatar
Paul McCarthy committed
670
671
672
673
1.13.3 (Friday February 8th 2019)
---------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
674
675
676
Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
677

678
* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
Paul McCarthy's avatar
Paul McCarthy committed
679
  image files that would subsequently be deleted.
Paul McCarthy's avatar
Paul McCarthy committed
680
* Fixed an issue in the :class:`.GiftiMesh` class, where
Paul McCarthy's avatar
Paul McCarthy committed
681
682
683
  ``numpy``/``nibabel`` was returning read-only index arrays.


Paul McCarthy's avatar
Paul McCarthy committed
684
685
686
687
688
689
690
691
1.13.2 (Friday November 30th 2018)
----------------------------------


Changed
^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
692
693
* The :meth:`.Image.resample` method now supports images with more than three
  dimensions.
Michiel Cottaar's avatar
Michiel Cottaar committed
694
695
696
697
* The :func:`fsl.utils.fslsub.submit` now returns the job-id as a string
  rather than a one-element tuple. It now also accepts a nested sequence
  of job ids rather than just a flat sequence. This will also changes the
  output from the function wrappers in :mod:`fsl.wrappers` if submitted.
698
699


Paul McCarthy's avatar
Paul McCarthy committed
700
701
Fixed
^^^^^
Paul McCarthy's avatar
Paul McCarthy committed
702

Paul McCarthy's avatar
Paul McCarthy committed
703
704
705
706
707
708

* Fix to the :class:`.ImageWrapper` regarding complex data types.


1.13.1 (Friday November 23rd 2018)
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
709
710


Paul McCarthy's avatar
Paul McCarthy committed
711
712
713
714
Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
715
* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
Paul McCarthy's avatar
Paul McCarthy committed
716
  class.
Paul McCarthy's avatar
Paul McCarthy committed
717
718
719
* Make sure that FEAT ``Cluster`` objects (created by the
  :func:`.loadClusterResults` function) contain ``p`` and ``logp`` attributes,
  even when cluster thresholding was not used.
Paul McCarthy's avatar
Paul McCarthy committed
720
721


Paul McCarthy's avatar
Paul McCarthy committed
722
723
1.13.0 (Thursday 22nd November 2018)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
724

Paul McCarthy's avatar
Paul McCarthy committed
725
726
727
728

Added
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
729
* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
Paul McCarthy's avatar
Paul McCarthy committed
730
  Craig).
Paul McCarthy's avatar
Paul McCarthy committed
731
* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
Paul McCarthy's avatar
Paul McCarthy committed
732
733
734
735
  Craig).


Changed
Paul McCarthy's avatar
Paul McCarthy committed
736
737
^^^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
738
739
* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
  interfaces (Martin Craig).
Paul McCarthy's avatar
Paul McCarthy committed
740
741
742
743
744
745
746


Fixed
^^^^^

* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
  input arguments.
Paul McCarthy's avatar
Paul McCarthy committed
747
748


Paul McCarthy's avatar
Paul McCarthy committed
749
750
1.12.0 (Sunday October 21st 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768


Changed
^^^^^^^


* The ``extract_noise`` script has been renamed to :mod:`.fsl_ents`.
* Increased the minimum required version of ``dcm2niix`` in the
  :mod:`fsl.data.dicom` module.


Deprecated
^^^^^^^^^^


* The ``extract_noise`` script.


Paul McCarthy's avatar
Paul McCarthy committed
769
770
771
772
773
774
775
776
777
778
779
1.11.1 (Friday September 14th 2018
----------------------------------


Fixed
^^^^^


* Fixed a Python 2 incompatibility in the :mod:`.settings` module.


Paul McCarthy's avatar
Paul McCarthy committed
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
1.11.0 (Thursday September 13th 2018)
-------------------------------------


Added
^^^^^


* A couple of new convenience functions to the :mod:`.settings` module.


Changed
^^^^^^^


* Development (test and documentation dependencies) are no longer listed
  in ``setup.py`` - they now need to be installed manually.
* Removed conda build infrastructure.


Paul McCarthy's avatar
Paul McCarthy committed
800
801
802
803
804
805
806
807
808
809
810
811
812
813
1.10.3 (Sunday September 9th 2018)
----------------------------------


Added
^^^^^


* The :func:`.parseVersionString` function accepts (and ignores) `local
  version identifer
  <https://www.python.org/dev/peps/pep-0440/#local-version-identifiers>`_
  strings.


Paul McCarthy's avatar
Paul McCarthy committed
814
815
816
817
818
819
820
821
822
823
824
825
1.10.2 (Friday September 7th 2018)
----------------------------------


Fixed
^^^^^


* The :meth:`.Image.save` method was not handling memory-mapped images
  correctly.


826
827
828
829
830
831
832
833
834
835
836
837
838
839
1.10.1 (Friday August 3rd 2018)
-------------------------------


Changed
^^^^^^^


* Minor adjustmenets to improve Windows compatibility.


Fixed
^^^^^

Paul McCarthy's avatar
Paul McCarthy committed
840
* The :mod:`.FEATImage.getCOPE` method was returning PE images.
841
842


843
844
1.10.0 (Wednesday July 18th 2018)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
845
846
847
848
849
850
851
852
853
854


Added
^^^^^


* A new script, :mod:`.extract_noise`, which can be used to extract ICA
  component time courses from a MELODIC ICA analysis.
* New :func:`.path.allFiles` function which returns all files underneath a
  directory.
855
* The :func:`.fileOrImage` and :func:`.fileOrArray` decorators now support
Paul McCarthy's avatar
Paul McCarthy committed
856
  loading of files which are specified with an output basename.
857
* New :mod:`.fast` wrapper function for the FSL FAST tool.
Paul McCarthy's avatar
Paul McCarthy committed
858
859
860
861
862
863
864
865
866
867
868


Changed
^^^^^^^


* When using the :func:`.run.run` function, the command output/error streams
  are now forwarded immediately.
* Removed dependency on ``pytest-runner``.


Paul McCarthy's avatar
Paul McCarthy committed
869
870
1.9.0 (Monday June 4th 2018)
----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904


Added
^^^^^


* New :meth:`.Image.data` property method, for easy access to image data
  as a ``numpy`` array.
* New ``log`` option to the :func:`.run.run` function, allowing more
  fine-grained control over sub-process output streams.
* New :meth:`.Platform.fsldevdir` property, allowing the ``$FSLDEVDIR``
  environment variable to be queried/changed.


Changed
^^^^^^^


* :meth:`.Image.ndims` has been renamed to :meth:`.Image.ndim`, to align
  more closely with ``numpy`` naming conventions.
* The ``err`` and ``ret`` parameters to the :func:`.run.run` function have
  been renamed to ``stderr`` and ``exitcode`` respectively.
* The :func:`.runfsl` function will give priority to the ``$FSLDEVDIR``
  environment variable if it is set.


Deprecated
^^^^^^^^^^


* :meth:`.Image.ndims`.
* The ``err`` and ``ret`` parameters to :func:`.run.run`.


Paul McCarthy's avatar
Paul McCarthy committed
905
906
907
908
909
910
911
912
913
914
915
916
1.8.1 (Friday May 11th 2018)
----------------------------


Changed
^^^^^^^


* The :func:`.fileOrImage` decorator function now accepts :class:`.Image`
  objects as well as ``nibabel`` image objects.


Paul McCarthy's avatar
Paul McCarthy committed
917
918
1.8.0 (Thursday May 3rd 2018)
-----------------------------
Paul McCarthy's avatar
Paul McCarthy committed
919
920
921
922
923
924
925
926
927
928


Added
^^^^^


* New :mod:`.wrappers` package, containing wrapper functions for a range of
  FSL tools.
* New :mod:`fsl.utils.run` module, to replace the :mod:`fsl.utils.callfsl`
  module.
Paul McCarthy's avatar
Paul McCarthy committed
929
* New :mod:`fsl.utils.fslsub` module, containing a :func:`.fslsub.submit`
Paul McCarthy's avatar
Paul McCarthy committed
930
  function which submits a cluster job via ``fsl_sub``.
Paul McCarthy's avatar
Paul McCarthy committed
931
932
* Assertions (in the :mod:`.assertions` module) can be disabled with the
  new :func:`.assertions.disabled` context manager.
Paul McCarthy's avatar
Paul McCarthy committed
933
934
* New :mod:`fsl.utils.parse_data` module containing various neuroimaging
  data constructors for use with ``argparse``.
Paul McCarthy's avatar
Paul McCarthy committed
935
936
* The :func:`.memoize.skipUnchanged` decorator has an ``invalidate`` function
  which allows its cache to be cleared.
Paul McCarthy's avatar
Paul McCarthy committed
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953


Changed
^^^^^^^


* The :func:`.tempdir` function has an option to not change to the newly
  created directory.


Deprecated
^^^^^^^^^^


* The :mod:`fsl.utils.callfsl` module (replaced with :mod:`fsl.utils.run`).


954
955
1.7.2 (Monday March 19th 2018)
------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
956
957
958
959
960
961


Added
^^^^^


962
963
* Added the :meth:`.MGHImage.voxToSurfMat` and related properties, giving
  access to the voxel-to-surface affine for an MGH image.
Paul McCarthy's avatar
Paul McCarthy committed
964
965


Paul McCarthy's avatar
Paul McCarthy committed
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
1.7.1 (Monday March 12th 2018)
------------------------------



Changed
^^^^^^^


* Adjusted :func:`.parseVersionString` so it accepts ``.dev*`` suffixes.


Fixed
^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
982
* Removed deprecated use of :func:`.imagewrapper.canonicalShape`.
Paul McCarthy's avatar
Paul McCarthy committed
983
984


Paul McCarthy's avatar
Paul McCarthy committed
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1.7.0 (Tuesday March 6th 2018)
------------------------------


Added
^^^^^


* The :mod:`fsl.utils.assertions` module contains a range of functions
  which can be used to assert that some condition is met.
* The :mod:`fsl.utils.ensure` module contains a range of functions (currently
  just one) which can be used to ensure that some condiution is met.


Changed
^^^^^^^


* The :mod:`.settings` module now saves its files in a format that is
  compatible with Python 2 and 3.
* The :func:`.tempdir` function now accepts a ``root`` argument, which
  specifies the location in which the temporary directory should be created.
* An image's data source can now be set via  :meth:`.Image.__init__`.
* :meth:`.MGHImage` objects now have a :meth:`.MGHImage.save` method.
* Adjustments to the ``conda`` package build and deployment process.
* The :func:`.ImageWrapper.canonicalShape` function has been moved
Paul McCarthy's avatar
Paul McCarthy committed
1011
  to the :mod:`.data.image` class.
Paul McCarthy's avatar
Paul McCarthy committed
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
* The :func:`.ImageWrapper.naninfrange` function has been moved
  into its own :mod:`.naninfrange` module.


Fixed
^^^^^


* Fixed a bug in the :class:`.MutexFactory` class.


Deprecated
^^^^^^^^^^


Paul McCarthy's avatar
Paul McCarthy committed
1027
* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
Paul McCarthy's avatar
Paul McCarthy committed
1028
1029
1030
1031
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
  module)


Paul McCarthy's avatar
Paul McCarthy committed
1032
1033
1034
1035
1036
1037
1038
1.6.8 (Monday February 12th 2018)
---------------------------------


* The `atlasq`, `immv`, `imcp` and `imglob` scripts suppress some warnings.


Paul McCarthy's avatar
Paul McCarthy committed
1039
1040
1041
1042
1043
1.6.7 (Friday February 9th 2018)
--------------------------------


* More further adjustments to the ``conda`` package build.
Paul McCarthy's avatar
Paul McCarthy committed
1044
* Adjustments to pypi source distribution - the ``requirements-extra.txt`` file
Paul McCarthy's avatar
Paul McCarthy committed
1045
1046
1047
  was not being included.


Paul McCarthy's avatar
Paul McCarthy committed
1048
1049
1050
1051
1052
1053
1054
1.6.6 (Thursday February 8th 2018)
----------------------------------


* Further adjustments to the ``conda`` package build.


Paul McCarthy's avatar
Paul McCarthy committed
1055
1056
1057
1058
1059
1060
1061
1.6.5 (Tuesday February 6th 2018)
---------------------------------


* Adjustments to the ``conda`` package build.


Paul McCarthy's avatar
Paul McCarthy committed
1062
1063
1064
1065
1066
1067
1068
1.6.4 (Monday February 5th 2018)
--------------------------------


* The :mod:`.platform` module emits a warning if it cannot import ``wx``.


Paul McCarthy's avatar
Paul McCarthy committed
1069
1070
1.6.3 (Friday February 2nd 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1071
1072
1073


* Minor enhancements to the :class:`.WeakFunctionRef` class.
Paul McCarthy's avatar
Paul McCarthy committed
1074
1075
1076
* Some bugfixes to the :mod:`fsl.utils.imcp` module, with respect to handling
  relative path names, moving file groups (e.g. `.img`/`.hdr` pairs), and
  non-existent directories.
Paul McCarthy's avatar
Paul McCarthy committed
1077
1078


Paul McCarthy's avatar
Paul McCarthy committed
1079
1080
1081
1082
1083
1084
1085
1086
1087
1.6.2 (Tuesday January 30th 2018)
---------------------------------


* Updates to the ``conda`` installation process.
* A new script is installed when ``fslpy`` is installed via ``pip`` or
  ``conda`` - ``atlasquery``, which emulates the FSL ``atlasquery`` tool.


Paul McCarthy's avatar
Paul McCarthy committed
1088
1089
1090
1091
1092
1093
1094
1095
1.6.1 (Monday January 29th 2018)
--------------------------------


* Removed ``lxml`` as a dependency - this was necessary in older versions of
  ``trimesh``.


Paul McCarthy's avatar
Paul McCarthy committed
1096
1097
1.6.0 (Friday January 26th 2018)
--------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1098
1099


Paul McCarthy's avatar
Paul McCarthy committed
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
* The new :class:`.Mesh` class is now the base class for all mesh types. It
  has been written to allow multiple sets of vertices to be associated with a
  mesh object (to support e.g. white matter, inflated, spherical models for a
  GIFTI/freeusrfer mesh).
* The new :class:`.VTKMesh` class must now be used for loading VTK model files,
  instead of the old :class:`.TriangleMesh` class.
* The new :class:`.Mesh` class uses the ``trimesh`` library
  (https://github.com/mikedh/trimesh) to perform various geometrical
  operations, accessible via new :meth:`.Mesh.rayIntersection`,
  :meth:`.Mesh.planeIntersection`, :meth:`.Mesh.nearestVertex` methods.
* The :class:`.Nifti` and :class:`.Mesh` classes have new methods allowing
  arbitrary metadata to be stored with the image, as key-value
  pairs. These are provided by a new mixin class, :class:`.Meta`.
Paul McCarthy's avatar
Paul McCarthy committed
1113
1114
* Freesurer surface files and vertex data can now be loaded via the
  :class:`.FreesurferMesh` class, in the new :mod:`.freesurfer` module.
Paul McCarthy's avatar
Paul McCarthy committed
1115
1116
1117
* Freesurfer ``mgz`` / ``mgh`` image files can now be loaded via the new
  :mod:`.mghimage` module. Internally, these image files are converted to NIFTI
  - the :class:`.MGHImage` class derives from the :class:`.Image` class.
Paul McCarthy's avatar
Paul McCarthy committed
1118
1119
1120
1121
1122
* Meta-data access methods on the :class:`.DicomImage` class have been
  deprecated, as their functionality is provided by the new :class:`.Meta`
  mixin.
* The :class:`.TriangleMesh` class has been deprecated in favour of the new
  :class:`.Mesh` class.
Paul McCarthy's avatar
Paul McCarthy committed
1123
* Optional dependencies ``wxpython``, ``indexed_gzip``, ``trimesh``, and
Paul McCarthy's avatar
Paul McCarthy committed
1124
1125
  ``rtree`` are now listed separately, so ``fslpy`` can be used without them
  (although relevant functionality will be disabled if they are not present).
Paul McCarthy's avatar
Paul McCarthy committed
1126
1127


Paul McCarthy's avatar
Paul McCarthy committed
1128
1129
1130
1131
1132
1133
1134
1.5.4 (Wednesday January 10th 2018)
-----------------------------------


* Actually included the fix that was supposed to be in version 1.5.3.


Paul McCarthy's avatar
Paul McCarthy committed
1135
1.5.3 (Tuesday January 9th 2018)
1136
1137
1138
1139
1140
1141
1142
--------------------------------


* Bug fix to :meth:`.ImageWrapper.__expandCoverage` - was not correctly handling
  large images with lots of ``nan`` values.


Paul McCarthy's avatar
Paul McCarthy committed
1143
1144
1145
1146
1147
1148
1149
1.5.2 (Tuesday January 2nd 2018)
--------------------------------


* Fixed issue with ``MANIFEST.in`` file.


Paul McCarthy's avatar
Paul McCarthy committed
1150
1151
1152
1153
1154
1155
1156
1.5.1 (Thursday December 14th 2017)
-----------------------------------


* Fixed bug in :func:`.dicom.scanDir` function related to data series ordering.


Paul McCarthy's avatar
Paul McCarthy committed
1157
1158
1.5.0 (Wednesday December 13th 2017)
------------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1159
1160
1161
1162
1163
1164


* New module :mod:`.dicom`, which provides a thin wrapper on top of Chris
  Rorden's `dcm2niix <https://github.com/rordenlab/dcm2niix>`_.
* New module :mod:`.tempdir`, which has a convenience function for creating
  temporary directories.
Paul McCarthy's avatar
Paul McCarthy committed
1165
1166
1167
* Fixed small issue in :meth:`.Image.dtype` - making sure that it access
  image data via the :class:`.ImageWrapper`, rather than via the `Nifti1Image`
  object.
Paul McCarthy's avatar
Paul McCarthy committed
1168
1169


Paul McCarthy's avatar
Paul McCarthy committed
1170
1171
1.4.2 (Tuesday December 5th 2017)
---------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1172
1173
1174
1175
1176


* New function :func:`.transform.rmsdev` function, which implements the RMS
  deviation equation for comparing two affine transformations (FMRIB Technical
  Report TR99MJ1, available at https://www.fmrib.ox.ac.uk/datasets/techrep/).
Paul McCarthy's avatar
Paul McCarthy committed
1177
* Some small bugfixes to the :mod:`.atlasq` and :mod:`.atlases` moduless.
Paul McCarthy's avatar
Paul McCarthy committed
1178
1179
1180


1.4.1 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1181
1182
1183
1184
1185
1186
----------------------------------


* Fixed bug in ``setup.py``.


Paul McCarthy's avatar
Paul McCarthy committed
1187
1.4.0 (Thursday November 9th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1188
----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1189

Paul McCarthy's avatar
Paul McCarthy committed
1190

Paul McCarthy's avatar
Paul McCarthy committed
1191
1192
* The :func:`.uniquePrefix` function now raises a :exc:`~.path.PathError`
  instead of a :exc:`.ValueError`, when an invalid path is provided.
Paul McCarthy's avatar
Paul McCarthy committed
1193
1194
1195
* The :mod:`fsl.utils.async` module is now deprecated, as ``async`` will
  become a reserved word in Python 3.7. It has been renamed to
  ``fsl.utils.idle``, with no other API changes.
Paul McCarthy's avatar
Paul McCarthy committed
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
* For image file pairs, the ``hdr`` extension now takes precedence over the
  ``img`` extension, when using the :func:`fsl.data.image.addExt` (and
  related) functions.
* The :func:`fsl.utils.path.addExt` function accepts a new parameter,
  ``unambiguous`` which causes it to allow an ambiguous prefix, and return
  all matching paths.
* New :mod:`~fsl.scripts.atlasq` application, intended to replace the FSL
  ``atlasquery`` tool.
* New :mod:`~fsl.scripts.imglob` application, intended to replace the FSL
  ``imglob`` tool.
* The :meth:`.Image.resample` method explicitly raises a ``ValueError``
  if incompatible shapes are provided.


Paul McCarthy's avatar
Paul McCarthy committed
1210
1.3.1 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1211
1212
1213
1214
1215
1216
1217
-----------------------------------


* Fixed bug in :meth:`.Platform.wxPlatform` causing it to always return
  ``WX_UNKNOWN``.


Paul McCarthy's avatar
Paul McCarthy committed
1218
1.3.0 (Wednesday October 25th 2017)
Paul McCarthy's avatar
Paul McCarthy committed
1219
-----------------------------------
Paul McCarthy's avatar
Paul McCarthy committed
1220
1221
1222
1223


* :class:`.Atlas` classes can now pass ``kwargs`` through to the
  :class:`.Image` constructor.
Paul McCarthy's avatar
Paul McCarthy committed
1224
1225
1226
* :class:`.LabelAtlas` image values no longer need to match the index of the
  label into the :class:`.AtlasDescription` ``labels`` list. This means that
  label atlas XML files may contain non-sequential label values.
Paul McCarthy's avatar
Paul McCarthy committed
1227
* :class:`.Cache` now implements ``__getitem__`` and ``__setitem__``
Paul McCarthy's avatar
Paul McCarthy committed
1228
1229
* The :func:`.image.read_segments` function (monkey-patched into ``nibabel``)
  is deprecated, as it is no longer necessary as of ``nibabel`` 2.2.0.
Paul McCarthy's avatar
Paul McCarthy committed
1230
1231
* :func:`.platform.isWidgetAlive` is deprecated in favour of an equivalent
  function in the ``fsleyes-widgets`` library.
Paul McCarthy's avatar
Paul McCarthy committed
1232
1233
* ``scipy`` is now explicitly listed as a requirement (this should have been
  done in 1.2.1).
Paul McCarthy's avatar
Paul McCarthy committed
1234
1235
1236
1237
1238
1239
1240



1.2.2 (Saturday October 21st 2017)
----------------------------------


Paul McCarthy's avatar
Paul McCarthy committed
1241
1242
* The :func:`.image.read_segments` function is only monkey-patched into
  ``nibabel`` 2.1.0, as it breaks when used with 2.2.0.
Paul McCarthy's avatar
Paul McCarthy committed
1243
1244
1245
1246
1247


1.2.1 (Saturday October 7th 2017)
---------------------------------

Paul McCarthy's avatar
Paul McCarthy committed
1248

Paul McCarthy's avatar
Paul McCarthy committed
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
* If an :class:`.Image` is passed an existing ``nibabel`` header object,
  it creates a copy, rather than using the original.
* New :meth:`.Image.resample` method, which resamples the image data to a
  different resolution.
* New :meth:`.LabelAtlas.coordLabel`, :meth:`.LabelAtlas.maskLabel`,
  :meth:`.ProbabilisticAtlas.coordProportions` and
  :meth:`.ProbabilisticAtlas.maskProportions` methods. The ``coord``
  methods perform coordinate queries in voxel or world coordinates,
  and the ``mask`` methods perform mask-based queries.


1.2.0 (Thursday September 21st 2017)
------------------------------------


* :meth:`fsl.data.image.Nifti.voxelsToScaledVoxels` method deprecated in
Paul McCarthy's avatar
Paul McCarthy committed
1265
  favour of new :meth:`.Nifti.voxToScaledVoxMat` and
Paul McCarthy's avatar
Paul McCarthy committed
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
  :meth:`Nifti.scaledVoxToVoxMat` properties.


1.1.0 (Monday September 11th 2017)
----------------------------------


* The :mod:`fsl` package is now a ``pkgutil``-style `namespace package
  <https://packaging.python.org/guides/packaging-namespace-packages/>`_, so it
  can be used for different projects.
* Updates to :class:`fsl.data.image.Nifti` and :class:`fsl.data.image.Image`
  to add support for images with more than 4 dimensions:
  - New ``ndims`` property
  - ``is4DImage`` method deprecated


1.0.5 (Thursday August 10th 2017)
---------------------------------


* New functions and further adjustments in :mod:`fsl.utils.transform` module:
Paul McCarthy's avatar
Paul McCarthy committed
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298

 - :func:`.transform.rotMatToAffine` converts a ``(3, 3)`` rotation matrix
   into a ``(4, 4)`` affine.
 - :func:`.transform.transformNormal` applies an affine transform to one or
   more vectors.
 - :func:`.transform.veclength` calculates the length of a vector
 - :func:`.transform.normalise` normalises a vector
 - :func:`.transform.scaleOffsetXform` adjusted to have more flexibility with
   respect to inputs.
 - :func:`.transform.decompose` can return rotations either as three
   axis-angles, or as a rotation matrix

Paul McCarthy's avatar
Paul McCarthy committed
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
* Updates to :class:`fsl.data.mesh.TriangleMesh` - ``vertices`` and ``indices``
  are now ``property`` attributes. New lazily generated ``normals`` and
  ``vnormals`` properties (face and vertex normals respectively). Option
  to ``__init__`` to fix the face winding order of a mesh.
* :func:`fsl.utils.memoize.memoize` decorator made into a class rather than a
  function. The new :class:`.Memoize` class has an ``invalidate`` method, which
  clears the cache.


1.0.4 (Friday July 14th 2017)
-----------------------------


* Python 2/3 compatibility fix to :mod:`fsl.utils.callfsl`.
* Fix to :func:`fsl.utils.transform.scaleOffsetXform` - accepts inputs
  that are not lists.
* :func:`fsl.utils.transform.compose` accepts either a sequence of three
  axis angles, or a ``(3, 3)`` rotation matrix.


1.0.3 (Sunday June 11th 2017)
-----------------------------


* Fix to :mod:`fsl.utils.async` which was breaking environments where multiple
  ``wx.App`` instances were being created.


1.0.2 (Thursday June 8th 2017)
------------------------------


* Python 2/3 compatibility fixes
* New :func:`fsl.version.patchVersion` function.


1.0.1 (Sunday 4th June 2017)
----------------------------


* New version number parsing functions in :mod:`fsl.version`.


1.0.0 (Saturday May 27th 2017)
------------------------------


* Removed many GUI-related modules - they have been moved to the
  ``fsleyes-widgets`` project. The following modules have been removed:
  - :mod:`fsl.utils.colourbarbitmap`
  - :mod:`fsl.utils.dialog`
  - :mod:`fsl.utils.imagepanel`
  - :mod:`fsl.utils.layout`
  - :mod:`fsl.utils.platform`
  - :mod:`fsl.utils.runwindow`
  - :mod:`fsl.utils.status`
  - :mod:`fsl.utils.textbitmap`
  - :mod:`fsl.utils.typedict`
  - :mod:`fsl.utils.webpage`
* :mod:`fsl.utils.settings` module rewritten. It no longer uses ``wx``,
  but instead stores plain-text and ``pickle`` files in the user's home
  directory.
* Software GL renderer test in :mod:`fsl.utils.platform` is more lenient
* New :class:`.AtlasLabel` class
* :meth:`.Image.__init__` allows arguments to be passed through to
  ``nibabel.load``.
* New :meth:`.Nifti.strval` method to handle escaped strings in NIFTI headers.
* Python 2/3 compatibility fixes


0.11.0 (Thursday April 20th 2017)
---------------------------------


* First public release as part of FSL 5.0.10